| Variant ID: vg0409081764 (JBrowse) | Variation Type: INDEL |
| Chromosome: chr04 | Position: 9081764 |
| Reference Allele: C | Alternative Allele: CT |
| Primary Allele: C | Secondary Allele: CT |
Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 1.00, others allele: 0.00, population size: 322. )
CCATAGTATATAATGCCCACTTTAGAGGTCTAAGATCCTCCCCTGCGACTACATTAATTGTAGGTGCCCTAAGATTCACATACCAGAGGGGCTTCCCATA[C/CT]
TTTTTTTAAGGTAAAACAAAGGCCAGTGTATTGAAAACTGGGATGGTTGAAGAAGCTGTAGATGAACTTGCGGCTATTTAGGTGAAGATATATGGCATCC
GGATGCCATATATCTTCACCTAAATAGCCGCAAGTTCATCTACAGCTTCTTCAACCATCCCAGTTTTCAATACACTGGCCTTTGTTTTACCTTAAAAAAA[G/AG]
TATGGGAAGCCCCTCTGGTATGTGAATCTTAGGGCACCTACAATTAATGTAGTCGCAGGGGAGGATCTTAGACCTCTAAAGTGGGCATTATATACTATGG
| Populations | Population Size | Frequency of C(primary allele) | Frequency of CT(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 99.90% | 0.10% | 0.00% | 0.00% | NA |
| All Indica | 2759 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| All Japonica | 1512 | 99.70% | 0.30% | 0.00% | 0.00% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica II | 465 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica III | 913 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica Intermediate | 786 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Temperate Japonica | 767 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Tropical Japonica | 504 | 99.00% | 1.00% | 0.00% | 0.00% | NA |
| Japonica Intermediate | 241 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0409081764 | C -> CT | LOC_Os04g16680.1 | upstream_gene_variant ; 3877.0bp to feature; MODIFIER | N | Average:56.546; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| vg0409081764 | C -> CT | LOC_Os04g16700.1 | downstream_gene_variant ; 3299.0bp to feature; MODIFIER | N | Average:56.546; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |
| vg0409081764 | C -> CT | LOC_Os04g16690.1 | intron_variant ; MODIFIER | N | Average:56.546; most accessible tissue: Minghui63 flag leaf, score: 79.676 | N | N | N | N |